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Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 3-methoxypyridine (Chem 443)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M ammonium sulfate, 23 % to 28 % PEG 3350, 0.1 M sodium citrate pH 4.8 to 5.3, 1 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.49 50.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.128 α = 90 b = 119.461 β = 91.03 c = 94.552 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944 2013-01-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 35.97 99.2 0.067 0.045 0.999 12.9 3.1 44048
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 98.3 0.471 0.326 0.857 2.3 2.8 4279
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3LC0 2.3 29.87 41781 2255 99.06 0.2155 0.214 0.2169 0.2416 0.2437 RANDOM 45.038
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.68 0.59 2.06 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.598 r_dihedral_angle_4_deg 16.517 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_1_deg 5.317 r_angle_refined_deg 1.124 r_mcangle_it 1.115 r_angle_other_deg 0.792 r_mcbond_it 0.657 r_mcbond_other 0.657 r_chiral_restr 0.059
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.598 r_dihedral_angle_4_deg 16.517 r_dihedral_angle_3_deg 14.201 r_dihedral_angle_1_deg 5.317 r_angle_refined_deg 1.124 r_mcangle_it 1.115 r_angle_other_deg 0.792 r_mcbond_it 0.657 r_mcbond_other 0.657 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6387 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 89
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing